rTRM

rTRM (regulatory Transcriptional Regulatory Modules) introduces an approach to decipher the complex networks of transcription factors (TFs), co-factors, and their interactions that form transcriptional regulatory modules (TRMs), crucial for regulating gene expression programs with precise spatiotemporal specificity. By integrating genomic information from TF binding, cell type-specific gene expression, and protein-protein interactions (PPIs), rTRM provides a comprehensive method for reconstructing TRMs tailored to various cell types, including embryonic stem cells (ESC), hematopoietic stem cells (HSC), neural progenitor cells, trophoblast stem cells, and different subsets of terminally differentiated CD4(+) T cells.

Topic

Protein interactions

Detail

  • Operation: Transcriptional regulatory element prediction

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.40.0

  • Credit: The Japan Society for the Promotion of Science (JSPS) through the WPI-IFReC Research Program.

  • Input: -

  • Output: -

  • Contact: Diego Diez diego10ruiz@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Systematic identification of transcriptional regulatory modules from protein-protein interaction networks.
  • Diez D, et al. Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. 2014; 42:e6. doi: 10.1093/nar/gkt913
  • https://doi.org/10.1093/nar/gkt913
  • PMID: 24137002
  • PMC: PMC3874207

Download and documentation

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